Mmpbsa calculation

User discussions
1

GROMACS version: 2023.3
GROMACS modification: Yes/No

I have run md simulation on Gromacs version 2023.3. Using those output files (.xtc .tpr .top) i have tried to do MMPBSA calculation but it always show me error . How can i do mmpbsa calculation using the output files of Gromacs version 2023.3 ?

Here’s the code link i have used for mmpbsa calculation

I gave the following command for calculation

mpirun -np 4 gmx_MMPBSA -O -i mmpbsa.in -cs NPT-MD.tpr -ci index.ndx -cg 1 13 -ct 30ns.xtc -cp topol.top

2

generate tpr for the desired version

3

can you please elaborate.

4

Try looking at the GMX_MMPBSA.log file, it gives more specific error messages at the end

5

You have not specified the output in the command line. See the Examples page where you can find examples for your system. The original code is as follows:
gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

What type of error do you have? May be it is because of the gromacs version incompatibility (gmx_mmpbsa uses it own older version of gromacs in condo environment) or some other reasons.

7

Error show that some energy terms are undefined.Please check the input structure and trajectory. Here’s the screenshot what does it actually shows.

Screenshot from 2024-08-23 15-01-43
Screenshot from 2024-08-23 15-01-432560×1336 376 KB

8

Have you used the same version of Gromacs in gmx_mmpbsa module and for molecular dynamics simulation? If your md files were created in newer version, that it is necessary to add a gmx_path variable to the mmpbsa.in file: The input file - gmx_MMPBSA Documentation